X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microfluidic Microbatch
pH 8.5
Temperature 296.0
Details 19.4% PEG 400, 43 mM Tris 8.5, 86 mM MgCl2, Microfluidic microbatch, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.97 α = 90
b = 141.27 β = 112.26
c = 84.01 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-07-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.73 50 99.3 0.045 -- -- 3.8 -- 177485 2.0 2.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.73 1.79 98.6 0.974 -- 1.7 3.7 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.74 40.23 -- -- -- 168491 8897 98.75 -- 0.17164 0.17037 0.19561 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.736 1.781 -- 595 11510 0.269 0.3 -- 91.79
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.107
Anisotropic B[1][1] -0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.05
Anisotropic B[2][2] 0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 12.382
r_symmetry_hbond_refined 0.19
r_mcangle_it 1.192
r_angle_refined_deg 1.159
r_gen_planes_refined 0.005
r_mcbond_other 0.146
r_bond_refined_d 0.009
r_scangle_it 3.378
r_bond_other_d 0.001
r_angle_other_deg 0.852
r_dihedral_angle_2_deg 34.208
r_scbond_it 2.011
r_symmetry_vdw_refined 0.354
r_dihedral_angle_4_deg 19.356
r_dihedral_angle_1_deg 5.224
r_xyhbond_nbd_refined 0.15
r_gen_planes_other 0.001
r_mcbond_it 0.604
r_chiral_restr 0.07
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11785
Nucleic Acid Atoms 0
Heterogen Atoms 121
Solvent Atoms 907

Software

Software
Software Name Purpose
HKL-2000 data collection
AMoRE phasing
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling